|
Name |
Accession |
Description |
Interval |
E-value |
| rad25 |
TIGR00603 |
DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
60-786 |
0e+00 |
|
DNA repair helicase rad25; All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273168 [Multi-domain] Cd Length: 732 Bit Score: 1125.27 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 60 DYRKDMPLKGDFTARPLWVAPDGHIFLESFSPVYKHARDFLIAISEPVCRPQHIHEYQLTAYSLYAAVSVGLQTKDIIEY 139
Cdd:TIGR00603 1 DYSKQLELKPDHGSRPLWVAPDGHIFLESFSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 140 LERLSKSQLPKGVITFVQMCTVSYGKVKLVLKHNRYFVESRHSDVMQKLLKDSVIQSCilddRVQPAQQTELPAQEKIKF 219
Cdd:TIGR00603 81 LGRLSKTPIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPC----RIDPTEEESLQTPTYGSK 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 220 SHGNENEKGVEKDGAAADGTAAAATDGkVPADIDEFYGKIDGDDEEDaeiRNLQLLTFEIKQETIETVQKRCIELEYPLL 299
Cdd:TIGR00603 157 EDFIINKPGFTGGASAGQLEANQGESA-VPKDIADFYELEEEEEDED---EETATHSFEIDQEQVEEVKKRCIELDYPLL 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 300 AEYDFRNDTLNPNLGIDLKPSTTLRPYQEKSLRKMFGNSRARSGVIVLPCGAGKTLVGVTAVTTVNKRCLVLANSNVSVE 379
Cdd:TIGR00603 233 EEYDFRNDTVNPDLNIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVE 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 380 QWRAQFKLWSTIQDKQLVRFTREAKDpAPSGADAtkpvVCISTYSMVAYSGRRTLQAEEAMKFIEKQEWGLLLLDEVHTI 459
Cdd:TIGR00603 313 QWKQQFKMWSTIDDSQICRFTSDAKE-RFHGEAG----VVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVV 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 460 PAKMFRRVLTIVQAHCKLGLTATLVREDDKITDLNFLIGPKIYEANWMELQKAGHIAKVQCAEVWCPMTSAFYSYYLRSQ 539
Cdd:TIGR00603 388 PAAMFRRVLTIVQAHCKLGLTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLREN 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 540 IARKLLLAVMNPNKFRICQFLIKFHERRNDKIIVFSDNVFALKRYAIEMQKPFLYGETSQNERMKILQNFQYNPRVNTIF 619
Cdd:TIGR00603 468 SRKRMLLYVMNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIF 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 620 VSKVADTSFDLPEANVLIQISAHGGSRRQEAQRLGRILRAKKHSTDQ-FNAFFYSLVSQDTVEMGYSRKRQRFLVNQGYA 698
Cdd:TIGR00603 548 LSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEeYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYS 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 699 YKVVNNLPGME-LEDLKLASKESQLQLLQQVLATSDADAEEEDVKEELADGTI-----------RISRREATMASMSGGQ 766
Cdd:TIGR00603 628 FKVITHLPGMDnESNLAYSSKEEQLELLQKVLLAGDLDAELEVLEGEFGSRALgasrsmssasgKAVRRGGSLSSLSGGD 707
|
730 740
....*....|....*....|....*
gi 17556358 767 ---GAQYHSKA--KAIAERHPLFKR 786
Cdd:TIGR00603 708 dmaYMEYRKPAikKSKKEVHPLFKK 732
|
|
| ERCC3_RAD25_C |
pfam16203 |
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ... |
509-747 |
7.75e-159 |
|
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases.
Pssm-ID: 406585 Cd Length: 248 Bit Score: 460.91 E-value: 7.75e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 509 LQKAGHIAKVQCAEVWCPMTSAFYSYYLRSQIARKLLLAVMNPNKFRICQFLIKFHERRNDKIIVFSDNVFALKRYAIEM 588
Cdd:pfam16203 1 LQEKGHIANVQCAEVWCPMTAEFYREYLRSKSRKKRLLYVMNPNKFRACQFLIRYHERRGDKIIVFSDNVFALKEYAKKL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 589 QKPFLYGETSQNERMKILQNFQYNPRVNTIFVSKVADTSFDLPEANVLIQISAHGGSRRQEAQRLGRILRAKKHSTDQ-F 667
Cdd:pfam16203 81 NKPYIYGGTSQAERMRILQNFKHNPNVNTIFLSKVGDTSIDLPEANVLIQISSHFGSRRQEAQRLGRILRAKRRSNDEgF 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 668 NAFFYSLVSQDTVEMGYSRKRQRFLVNQGYAYKVVNNLPGME-LEDLKLASKESQLQLLQQVLATSDADAEEEDVKEELA 746
Cdd:pfam16203 161 NAFFYSLVSKDTQEMYYSTKRQQFLVDQGYAFKVITNLAGMEdEENLAYSTKEEQLELLQKVLAANDTDAEEEVIADDLG 240
|
.
gi 17556358 747 D 747
Cdd:pfam16203 241 K 241
|
|
| DEXHc_XPB |
cd18029 |
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ... |
315-489 |
8.76e-102 |
|
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350787 [Multi-domain] Cd Length: 169 Bit Score: 310.77 E-value: 8.76e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 315 IDLKPSTTLRPYQEKSLRKMFGNSRARSGVIVLPCGAGKTLVGVTAVTTVNKRCLVLANSNVSVEQWRAQFKLWSTIQDK 394
Cdd:cd18029 1 IDLKPSTQLRPYQEKALSKMFGNGRARSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 395 QLVRFTREAKDPAPsgadatKPVVCISTYSMVAYSGRRTLQAEEAMKFIEKQEWGLLLLDEVHTIPAKMFRRVLTIVQAH 474
Cdd:cd18029 81 QIGRFTSDKKEIFP------EAGVTVSTYSMLANTRKRSPESEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAH 154
|
170
....*....|....*
gi 17556358 475 CKLGLTATLVREDDK 489
Cdd:cd18029 155 CKLGLTATLVREDDK 169
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
261-757 |
7.80e-61 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 215.66 E-value: 7.80e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 261 GDDEEDAEIRNLQLLTFEIKQETIETVQKRCIELEYPLLAEYDFRNDTLNPNlGIDLKPSTTLRPYQEKSLRKMFG--NS 338
Cdd:COG1061 20 LLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAG-DEASGTSFELRPYQQEALEALLAalER 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 339 RARSGVIVLPCGAGKTLVGVTAV--TTVNKRCLVLANSNVSVEQWRAQFKlwstiqdkqlvRFTREAkdPAPSGADATKP 416
Cdd:COG1061 99 GGGRGLVVAPTGTGKTVLALALAaeLLRGKRVLVLVPRRELLEQWAEELR-----------RFLGDP--LAGGGKKDSDA 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 417 VVCISTYSmvaysgrrTLQAEEAMKFIEKqEWGLLLLDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKITDLNFL 496
Cdd:COG1061 166 PITVATYQ--------SLARRAHLDELGD-RFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGREILLFLF 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 497 IGpKIYEANWMELQKAGHIAKVQCAEVWCPMTSAFYSYYLRSQIARKlLLAVMNPNKFRICQFLIKFHeRRNDKIIVFSD 576
Cdd:COG1061 237 DG-IVYEYSLKEAIEDGYLAPPEYYGIRVDLTDERAEYDALSERLRE-ALAADAERKDKILRELLREH-PDDRKTLVFCS 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 577 NVFALKRYAIEMQK-----PFLYGETSQNERMKILQNFQyNPRVNTIFVSKVADTSFDLPEANVLIQISAHgGSRRQEAQ 651
Cdd:COG1061 314 SVDHAEALAELLNEagiraAVVTGDTPKKEREEILEAFR-DGELRILVTVDVLNEGVDVPRLDVAILLRPT-GSPREFIQ 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 652 RLGRILRAKKHSTDqfnAFFYSLVSQDTVEMGYSRKRQRFLVnqGYAYKVvnnlpgMELEDLKLASKESQLQLLQQVLAT 731
Cdd:COG1061 392 RLGRGLRPAPGKED---ALVYDFVGNDVPVLEELAKDLRDLA--GYRVEF------LDEEESEELALLIAVKPALEVKGE 460
|
490 500
....*....|....*....|....*.
gi 17556358 732 SDADAEEEDVKEELADGTIRISRREA 757
Cdd:COG1061 461 LEEELLEELELLEDALLLVLAELLLL 486
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
315-495 |
9.62e-19 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 85.24 E-value: 9.62e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 315 IDLKPSTTLRPYQEKSLRKMFgnSRARSGVIVLPCGAGKTLVGVTAV-----TTVNKRCLVLANSNVSVEQWRAQFKLWS 389
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALL--SGLRDVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 390 TIQD-KQLVRFTREAKDPAPSGADATKPVVCISTYSMVAYSGRRtlqaeeamKFIEKQEWGLLLLDEVHTIPAKMFRRVL 468
Cdd:smart00487 79 PSLGlKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLEN--------DKLSLSNVDLVILDEAHRLLDGGFGDQL 150
|
170 180 190
....*....|....*....|....*....|..
gi 17556358 469 TIV-----QAHCKLGLTATLVREDDKITDLNF 495
Cdd:smart00487 151 EKLlkllpKNVQLLLLSATPPEEIENLLELFL 182
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
324-422 |
7.89e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 39.86 E-value: 7.89e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 324 RPYQEKslrkMFGNSRARSGVIVLPCGAGKTLVG--VTA--VTTVNKRCLVLANSNVSVEQWRAQFKLWSTIQDKQLVRF 399
Cdd:PRK13766 17 RLYQQL----LAATALKKNTLVVLPTGLGKTAIAllVIAerLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVF 92
|
90 100
....*....|....*....|...
gi 17556358 400 TREAKdPAPSGADATKPVVCIST 422
Cdd:PRK13766 93 TGEVS-PEKRAELWEKAKVIVAT 114
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rad25 |
TIGR00603 |
DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
60-786 |
0e+00 |
|
DNA repair helicase rad25; All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273168 [Multi-domain] Cd Length: 732 Bit Score: 1125.27 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 60 DYRKDMPLKGDFTARPLWVAPDGHIFLESFSPVYKHARDFLIAISEPVCRPQHIHEYQLTAYSLYAAVSVGLQTKDIIEY 139
Cdd:TIGR00603 1 DYSKQLELKPDHGSRPLWVAPDGHIFLESFSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 140 LERLSKSQLPKGVITFVQMCTVSYGKVKLVLKHNRYFVESRHSDVMQKLLKDSVIQSCilddRVQPAQQTELPAQEKIKF 219
Cdd:TIGR00603 81 LGRLSKTPIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKDPVIAPC----RIDPTEEESLQTPTYGSK 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 220 SHGNENEKGVEKDGAAADGTAAAATDGkVPADIDEFYGKIDGDDEEDaeiRNLQLLTFEIKQETIETVQKRCIELEYPLL 299
Cdd:TIGR00603 157 EDFIINKPGFTGGASAGQLEANQGESA-VPKDIADFYELEEEEEDED---EETATHSFEIDQEQVEEVKKRCIELDYPLL 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 300 AEYDFRNDTLNPNLGIDLKPSTTLRPYQEKSLRKMFGNSRARSGVIVLPCGAGKTLVGVTAVTTVNKRCLVLANSNVSVE 379
Cdd:TIGR00603 233 EEYDFRNDTVNPDLNIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVE 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 380 QWRAQFKLWSTIQDKQLVRFTREAKDpAPSGADAtkpvVCISTYSMVAYSGRRTLQAEEAMKFIEKQEWGLLLLDEVHTI 459
Cdd:TIGR00603 313 QWKQQFKMWSTIDDSQICRFTSDAKE-RFHGEAG----VVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVV 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 460 PAKMFRRVLTIVQAHCKLGLTATLVREDDKITDLNFLIGPKIYEANWMELQKAGHIAKVQCAEVWCPMTSAFYSYYLRSQ 539
Cdd:TIGR00603 388 PAAMFRRVLTIVQAHCKLGLTATLVREDDKITDLNFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLREN 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 540 IARKLLLAVMNPNKFRICQFLIKFHERRNDKIIVFSDNVFALKRYAIEMQKPFLYGETSQNERMKILQNFQYNPRVNTIF 619
Cdd:TIGR00603 468 SRKRMLLYVMNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFQHNPKVNTIF 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 620 VSKVADTSFDLPEANVLIQISAHGGSRRQEAQRLGRILRAKKHSTDQ-FNAFFYSLVSQDTVEMGYSRKRQRFLVNQGYA 698
Cdd:TIGR00603 548 LSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEeYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYS 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 699 YKVVNNLPGME-LEDLKLASKESQLQLLQQVLATSDADAEEEDVKEELADGTI-----------RISRREATMASMSGGQ 766
Cdd:TIGR00603 628 FKVITHLPGMDnESNLAYSSKEEQLELLQKVLLAGDLDAELEVLEGEFGSRALgasrsmssasgKAVRRGGSLSSLSGGD 707
|
730 740
....*....|....*....|....*
gi 17556358 767 ---GAQYHSKA--KAIAERHPLFKR 786
Cdd:TIGR00603 708 dmaYMEYRKPAikKSKKEVHPLFKK 732
|
|
| ERCC3_RAD25_C |
pfam16203 |
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ... |
509-747 |
7.75e-159 |
|
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases.
Pssm-ID: 406585 Cd Length: 248 Bit Score: 460.91 E-value: 7.75e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 509 LQKAGHIAKVQCAEVWCPMTSAFYSYYLRSQIARKLLLAVMNPNKFRICQFLIKFHERRNDKIIVFSDNVFALKRYAIEM 588
Cdd:pfam16203 1 LQEKGHIANVQCAEVWCPMTAEFYREYLRSKSRKKRLLYVMNPNKFRACQFLIRYHERRGDKIIVFSDNVFALKEYAKKL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 589 QKPFLYGETSQNERMKILQNFQYNPRVNTIFVSKVADTSFDLPEANVLIQISAHGGSRRQEAQRLGRILRAKKHSTDQ-F 667
Cdd:pfam16203 81 NKPYIYGGTSQAERMRILQNFKHNPNVNTIFLSKVGDTSIDLPEANVLIQISSHFGSRRQEAQRLGRILRAKRRSNDEgF 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 668 NAFFYSLVSQDTVEMGYSRKRQRFLVNQGYAYKVVNNLPGME-LEDLKLASKESQLQLLQQVLATSDADAEEEDVKEELA 746
Cdd:pfam16203 161 NAFFYSLVSKDTQEMYYSTKRQQFLVDQGYAFKVITNLAGMEdEENLAYSTKEEQLELLQKVLAANDTDAEEEVIADDLG 240
|
.
gi 17556358 747 D 747
Cdd:pfam16203 241 K 241
|
|
| DEXHc_XPB |
cd18029 |
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ... |
315-489 |
8.76e-102 |
|
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350787 [Multi-domain] Cd Length: 169 Bit Score: 310.77 E-value: 8.76e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 315 IDLKPSTTLRPYQEKSLRKMFGNSRARSGVIVLPCGAGKTLVGVTAVTTVNKRCLVLANSNVSVEQWRAQFKLWSTIQDK 394
Cdd:cd18029 1 IDLKPSTQLRPYQEKALSKMFGNGRARSGVIVLPCGAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 395 QLVRFTREAKDPAPsgadatKPVVCISTYSMVAYSGRRTLQAEEAMKFIEKQEWGLLLLDEVHTIPAKMFRRVLTIVQAH 474
Cdd:cd18029 81 QIGRFTSDKKEIFP------EAGVTVSTYSMLANTRKRSPESEKFMEFITEREWGLIILDEVHVVPAPMFRRVLTLQKAH 154
|
170
....*....|....*
gi 17556358 475 CKLGLTATLVREDDK 489
Cdd:cd18029 155 CKLGLTATLVREDDK 169
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
520-675 |
7.06e-83 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350176 [Multi-domain] Cd Length: 153 Bit Score: 260.64 E-value: 7.06e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 520 CAEVWCPMTSAFYSYYLRSQIARK-LLLAVMNPNKFRICQFLIKFHERrNDKIIVFSDNVFALKRYAIEMQKPFLYGETS 598
Cdd:cd18789 1 CAEIRCPMTPEFYREYLGLGAHRKrRLLAAMNPNKLRALEELLKRHEQ-GDKIIVFTDNVEALYRYAKRLLKPFITGETP 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17556358 599 QNERMKILQNFQYNPrVNTIFVSKVADTSFDLPEANVLIQISAHGGSRRQEAQRLGRILRAKKHStdQFNAFFYSLV 675
Cdd:cd18789 80 QSEREEILQNFREGE-YNTLVVSKVGDEGIDLPEANVAIQISGHGGSRRQEAQRLGRILRPKKGG--GKNAFFYSLV 153
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
261-757 |
7.80e-61 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 215.66 E-value: 7.80e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 261 GDDEEDAEIRNLQLLTFEIKQETIETVQKRCIELEYPLLAEYDFRNDTLNPNlGIDLKPSTTLRPYQEKSLRKMFG--NS 338
Cdd:COG1061 20 LLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAG-DEASGTSFELRPYQQEALEALLAalER 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 339 RARSGVIVLPCGAGKTLVGVTAV--TTVNKRCLVLANSNVSVEQWRAQFKlwstiqdkqlvRFTREAkdPAPSGADATKP 416
Cdd:COG1061 99 GGGRGLVVAPTGTGKTVLALALAaeLLRGKRVLVLVPRRELLEQWAEELR-----------RFLGDP--LAGGGKKDSDA 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 417 VVCISTYSmvaysgrrTLQAEEAMKFIEKqEWGLLLLDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKITDLNFL 496
Cdd:COG1061 166 PITVATYQ--------SLARRAHLDELGD-RFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGREILLFLF 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 497 IGpKIYEANWMELQKAGHIAKVQCAEVWCPMTSAFYSYYLRSQIARKlLLAVMNPNKFRICQFLIKFHeRRNDKIIVFSD 576
Cdd:COG1061 237 DG-IVYEYSLKEAIEDGYLAPPEYYGIRVDLTDERAEYDALSERLRE-ALAADAERKDKILRELLREH-PDDRKTLVFCS 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 577 NVFALKRYAIEMQK-----PFLYGETSQNERMKILQNFQyNPRVNTIFVSKVADTSFDLPEANVLIQISAHgGSRRQEAQ 651
Cdd:COG1061 314 SVDHAEALAELLNEagiraAVVTGDTPKKEREEILEAFR-DGELRILVTVDVLNEGVDVPRLDVAILLRPT-GSPREFIQ 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 652 RLGRILRAKKHSTDqfnAFFYSLVSQDTVEMGYSRKRQRFLVnqGYAYKVvnnlpgMELEDLKLASKESQLQLLQQVLAT 731
Cdd:COG1061 392 RLGRGLRPAPGKED---ALVYDFVGNDVPVLEELAKDLRDLA--GYRVEF------LDEEESEELALLIAVKPALEVKGE 460
|
490 500
....*....|....*....|....*.
gi 17556358 732 SDADAEEEDVKEELADGTIRISRREA 757
Cdd:COG1061 461 LEEELLEELELLEDALLLVLAELLLL 486
|
|
| Helicase_C_3 |
pfam13625 |
Helicase conserved C-terminal domain; This domain family is found in a wide variety of ... |
76-199 |
6.46e-43 |
|
Helicase conserved C-terminal domain; This domain family is found in a wide variety of helicases and helicase-related proteins.
Pssm-ID: 463939 [Multi-domain] Cd Length: 121 Bit Score: 151.50 E-value: 6.46e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 76 LWVAPDGHIFLESfsPVYKHARDFLIAISEPVCRpQHIHEYQLTAYSLYAAVSVGLQTKDIIEYLERLSKSQLPKGVITF 155
Cdd:pfam13625 1 LIVQADLTILLPG--PLAPEARDFLAAFAELESR-GHAHTYRLTPLSLRRALDAGLTAEDILDFLERHSKYPVPQALEYL 77
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 17556358 156 VQMCTVSYGKVKLVLkHNRYFVESRHSDVMQKLLKDSVIQSCIL 199
Cdd:pfam13625 78 IRDVARRHGRLRLGL-GASSYLRSDDPAVLAELLADPRIAPLGL 120
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
323-483 |
8.69e-36 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 132.04 E-value: 8.69e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 323 LRPYQEKSLRKMFGNSRARSGVIVLPCGAGKTLVGVTA-VTTVNKRCLVLANSNVSVEQWRAQFKLWSTiqDKQLVRFTR 401
Cdd:cd17926 1 LRPYQEEALEAWLAHKNNRRGILVLPTGSGKTLTALALiAYLKELRTLIVVPTDALLDQWKERFEDFLG--DSSIGLIGG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 402 EAKDpapsgADATKPVVcISTYSMVaysgrrTLQAEEAMKFieKQEWGLLLLDEVHTIPAKMFRRVLTIVQAHCKLGLTA 481
Cdd:cd17926 79 GKKK-----DFDDANVV-VATYQSL------SNLAEEEKDL--FDQFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTA 144
|
..
gi 17556358 482 TL 483
Cdd:cd17926 145 TP 146
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
315-495 |
9.62e-19 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 85.24 E-value: 9.62e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 315 IDLKPSTTLRPYQEKSLRKMFgnSRARSGVIVLPCGAGKTLVGVTAV-----TTVNKRCLVLANSNVSVEQWRAQFKLWS 389
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALL--SGLRDVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 390 TIQD-KQLVRFTREAKDPAPSGADATKPVVCISTYSMVAYSGRRtlqaeeamKFIEKQEWGLLLLDEVHTIPAKMFRRVL 468
Cdd:smart00487 79 PSLGlKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLEN--------DKLSLSNVDLVILDEAHRLLDGGFGDQL 150
|
170 180 190
....*....|....*....|....*....|..
gi 17556358 469 TIV-----QAHCKLGLTATLVREDDKITDLNF 495
Cdd:smart00487 151 EKLlkllpKNVQLLLLSATPPEEIENLLELFL 182
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
322-485 |
3.18e-16 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 76.94 E-value: 3.18e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 322 TLRPYQE---KSLRKMFGNSRARsGVIVLPCGAGKTLVGVTAVTTVNK-----RCLVLANSNVSVEQWRAQFKLWSTIQD 393
Cdd:pfam04851 3 ELRPYQIeaiENLLESIKNGQKR-GLIVMATGSGKTLTAAKLIARLFKkgpikKVLFLVPRKDLLEQALEEFKKFLPNYV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 394 KQLVRFTREAKDPAPSGADatkpvVCISTYSMVaySGRRTLQAEEAmkfiEKQEWGLLLLDEVHTIPAKMFRRVLTIVQA 473
Cdd:pfam04851 82 EIGEIISGDKKDESVDDNK-----IVVTTIQSL--YKALELASLEL----LPDFFDVIIIDEAHRSGASSYRNILEYFKP 150
|
170
....*....|..
gi 17556358 474 HCKLGLTATLVR 485
Cdd:pfam04851 151 AFLLGLTATPER 162
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
552-660 |
1.59e-12 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 64.54 E-value: 1.59e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 552 NKFRICQFLIKFHerRNDKIIVFSDNVFALKRYAIEMQKPF----LYGETSQNERMKILQNFQyNPRVNTIFVSKVADTS 627
Cdd:pfam00271 1 EKLEALLELLKKE--RGGKVLIFSQTKKTLEAELLLEKEGIkvarLHGDLSQEEREEILEDFR-KGKIDVLVATDVAERG 77
|
90 100 110
....*....|....*....|....*....|...
gi 17556358 628 FDLPEANVLIQISAHgGSRRQEAQRLGRILRAK 660
Cdd:pfam00271 78 LDLPDVDLVINYDLP-WNPASYIQRIGRAGRAG 109
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
323-489 |
3.04e-12 |
|
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350790 [Multi-domain] Cd Length: 163 Bit Score: 65.28 E-value: 3.04e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 323 LRPYQEKSLRKMFgNSRA---RSGVIVLPCGAGKTLVGVTAV-----TTVNKRCLVLANSNVSVEQwrAQFKLWSTIQDK 394
Cdd:cd18032 1 PRYYQQEAIEALE-EAREkgqRRALLVMATGTGKTYTAAFLIkrlleANRKKRILFLAHREELLEQ--AERSFKEVLPDG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 395 QLVRFTREAKDPapSGADatkpvVCISTY-SMVAysgrrtlqAEEAMKFiEKQEWGLLLLDEVHTIPAKMFRRVLtivqA 473
Cdd:cd18032 78 SFGNLKGGKKKP--DDAR-----VVFATVqTLNK--------RKRLEKF-PPDYFDLIIIDEAHHAIASSYRKIL----E 137
|
170 180
....*....|....*....|
gi 17556358 474 HCK----LGLTATLVREDDK 489
Cdd:cd18032 138 YFEpaflLGLTATPERTDGL 157
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
74-691 |
1.47e-11 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 67.94 E-value: 1.47e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 74 RPLWVAPDGHIFLESFSPVYKHARDFLIAISEPvcRPQHIHEYQLTAYSLYAAVSVGLQTKDIIEYLERLSKSQLPKGVI 153
Cdd:COG0553 1 LLLLLLLLALGALGLLLTELLLLLRLGALLLEL--VLARELLLLLLAADALLLLALLLLLELLLLLAALLLLALLLLALS 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 154 TFVQMCTVSYGKVKLVLKHNRYFVESRHSDVMQKLLKDSVIQSCILDDRVQPAQQTELPAQEKIKFSHGNENEKGVEKDG 233
Cdd:COG0553 79 ALALLLLRLLLALLLLALLLLLAGLLALALLLLALLGLLLSLALLLLLLLLLLLLLLALLLVLLAALLLLLLLLLLLALL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 234 AAADGTAAAATDGKVPADIDEFYGKIDGDDEEDAEIRNLQLLTFEIKQETIETVQKRCIELEYPLLAEYDFRNDTLNPNL 313
Cdd:COG0553 159 LGRLLLLALLLLALEALLLLGLLLALALLALLELALLAAEAELLLLLELLLELELLAEAAVDAFRLRRLREALESLPAGL 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 314 GidlkpsTTLRPYQEKSLRKMFGNSRARSGVI----VlpcGAGKTLVGVTAV-----TTVNKRCLVLANSNVsVEQWRAQ 384
Cdd:COG0553 239 K------ATLRPYQLEGAAWLLFLRRLGLGGLladdM---GLGKTIQALALLlelkeRGLARPVLIVAPTSL-VGNWQRE 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 385 FKLWSTiqDKQLVRFTREAKDPAPSGADATKPVVcISTYSMVaysgRRTLQAeeamkfIEKQEWGLLLLDEVHTI---PA 461
Cdd:COG0553 309 LAKFAP--GLRVLVLDGTRERAKGANPFEDADLV-ITSYGLL----RRDIEL------LAAVDWDLVILDEAQHIknpAT 375
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 462 KMFRRVLTIvQAHCKLGLTATLV--REDD-----KITDLNFLIGPKIYEANWMELQKAGHIA-----------------K 517
Cdd:COG0553 376 KRAKAVRAL-KARHRLALTGTPVenRLEElwsllDFLNPGLLGSLKAFRERFARPIEKGDEEalerlrrllrpfllrrtK 454
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 518 VQCAE---------VWCPMTSAFYSYY--LRSQIARKLLLAVMNPNKF----------RIC----QFL----------IK 562
Cdd:COG0553 455 EDVLKdlpekteetLYVELTPEQRALYeaVLEYLRRELEGAEGIRRRGlilaaltrlrQICshpaLLLeegaelsgrsAK 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 563 FHE---------RRNDKIIVFS---DNVFALKRY--AIEMQKPFLYGETSQNERMKILQNFQYNPRVNTIFVS-KVADTS 627
Cdd:COG0553 535 LEAllelleellAEGEKVLVFSqftDTLDLLEERleERGIEYAYLHGGTSAEERDELVDRFQEGPEAPVFLISlKAGGEG 614
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17556358 628 FDLPEANVLIQIS-----AHggsrrqEAQRLGRILR--AKKhstdqfNAFFYSLVSQDTVEMG----YSRKRQRF 691
Cdd:COG0553 615 LNLTAADHVIHYDlwwnpAV------EEQAIDRAHRigQTR------DVQVYKLVAEGTIEEKilelLEEKRALA 677
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
592-660 |
3.24e-10 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 56.84 E-value: 3.24e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17556358 592 FLYGETSQNERMKILQNFQyNPRVNTIFVSKVADTSFDLPEANVLIQISAHgGSRRQEAQRLGRILRAK 660
Cdd:smart00490 16 RLHGGLSQEEREEILDKFN-NGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAGRAG 82
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
323-482 |
1.23e-09 |
|
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350677 [Multi-domain] Cd Length: 182 Bit Score: 58.35 E-value: 1.23e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 323 LRPYQEKSLRKMFGNSRARSGVIVLPC-GAGKTLVGVTAVTTV------NKRCLVLANSNVsVEQWRAQFKLWS------ 389
Cdd:cd17919 1 LRPYQLEGLNFLLELYENGPGGILADEmGLGKTLQAIAFLAYLlkegkeRGPVLVVCPLSV-LENWEREFEKWTpdlrvv 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 390 TIQDKQLVRFTREAKDPAPSgADatkpvVCISTYSMVAYSGRRtlqaeeamkfIEKQEWGLLLLDEVHTI---PAKMFRR 466
Cdd:cd17919 80 VYHGSQRERAQIRAKEKLDK-FD-----VVLTTYETLRRDKAS----------LRKFRWDLVVVDEAHRLknpKSQLSKA 143
|
170
....*....|....*.
gi 17556358 467 VLTIvQAHCKLGLTAT 482
Cdd:cd17919 144 LKAL-RAKRRLLLTGT 158
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
343-482 |
5.07e-05 |
|
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 43.93 E-value: 5.07e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 343 GVIVLPCGAGKTLVG----VTAVTTVNKRCLVLANSNVSVEQWRAQFKLWSTIQDKqLVRFTREAKDPAPSGADATKPVV 418
Cdd:cd00046 4 VLITAPTGSGKTLAAllaaLLLLLKKGKKVLVLVPTKALALQTAERLRELFGPGIR-VAVLVGGSSAEEREKNKLGDADI 82
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17556358 419 CISTYSMVAYSGRRTLQAEEAmkfiekqEWGLLLLDEVHTIPAKMfRRVLTIVQAHCKL--------GLTAT 482
Cdd:cd00046 83 IIATPDMLLNLLLREDRLFLK-------DLKLIIVDEAHALLIDS-RGALILDLAVRKAglknaqviLLSAT 146
|
|
| SF2_C_SNF |
cd18793 |
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
553-658 |
1.36e-04 |
|
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350180 [Multi-domain] Cd Length: 135 Bit Score: 42.46 E-value: 1.36e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 553 KFRICQFLIKFHERRNDKIIVFS---DNVFALKRYAIEMQKPFLY--GETSQNERMKILQNFQYNPRVNTIFVS-KVADT 626
Cdd:cd18793 12 KLEALLELLEELREPGEKVLIFSqftDTLDILEEALRERGIKYLRldGSTSSKERQKLVDRFNEDPDIRVFLLStKAGGV 91
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 17556358 627 SFDLPEANVLI--------QIsahggsrrqEAQRLGRILR 658
Cdd:cd18793 92 GLNLTAANRVIlydpwwnpAV---------EEQAIDRAHR 122
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
322-459 |
4.84e-04 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 41.86 E-value: 4.84e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 322 TLRPYQEKSLRKmFGNSRaRSGVIVLPCGAGKTLVG----VTAVTTVNKRCLVLANSNVSVEQWRAQFKLWSTIQDKQLV 397
Cdd:cd17921 1 LLNPIQREALRA-LYLSG-DSVLVSAPTSSGKTLIAelaiLRALATSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVG 78
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17556358 398 RFTReakDPAPSGADATKPVVCISTY----SMVAYSGRRTLqaeeamkfiekQEWGLLLLDEVHTI 459
Cdd:cd17921 79 LLTG---DPSVNKLLLAEADILVATPekldLLLRNGGERLI-----------QDVRLVVVDEAHLI 130
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
569-672 |
6.78e-04 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 38.84 E-value: 6.78e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 569 DKIIVFSDNVFALKRYAiemqkpflygetsqnERMKILqnfqynprVNTifvsKVADTSFDLPEANVLIQISAHGgSRRQ 648
Cdd:cd18785 4 VKIIVFTNSIEHAEEIA---------------SSLEIL--------VAT----NVLGEGIDVPSLDTVIFFDPPS-SAAS 55
|
90 100
....*....|....*....|....
gi 17556358 649 EAQRLGRILRAKKhstDQFNAFFY 672
Cdd:cd18785 56 YIQRVGRAGRGGK---DEGEVILF 76
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
321-380 |
1.15e-03 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 41.10 E-value: 1.15e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 321 TTLRPYQEKSLRKmfgnSRARSGVIVLPCGAGKTLVGV----------TAVTTVNKRCLVLANSNVSVEQ 380
Cdd:cd18034 1 FTPRSYQLELFEA----ALKRNTIVVLPTGSGKTLIAVmlikemgelnRKEKNPKKRAVFLVPTVPLVAQ 66
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
324-490 |
2.39e-03 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 41.25 E-value: 2.39e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 324 RPYQEKslrkMFGNSRARSGVIVLPCGAGKTLVG--VTA--VTTVNKRCLVLANSNVSVEQWRAQFKLWSTIQDKQLVRF 399
Cdd:COG1111 5 RLYQLN----LAASALRKNTLVVLPTGLGKTAVAllVIAerLHKKGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 400 TREAKdPAPSGADATKPVVCISTYSMVA---YSGRrtlqaeeamkfIEKQEWGLLLLDEVH--------TIPAKMFRRvl 468
Cdd:COG1111 81 TGEVS-PEKRKELWEKARIIVATPQVIEndlIAGR-----------IDLDDVSLLIFDEAHravgnyayVYIAERYHE-- 146
|
170 180
....*....|....*....|....
gi 17556358 469 tivQAHCKL--GLTATLVREDDKI 490
Cdd:COG1111 147 ---DAKDPLilGMTASPGSDEEKI 167
|
|
| DEXHc_ATRX-like |
cd18007 |
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ... |
323-484 |
4.11e-03 |
|
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350765 [Multi-domain] Cd Length: 239 Bit Score: 39.58 E-value: 4.11e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 323 LRPYQEKSLRKM-------FGNSRARSGVIVLPC-GAGKTLVGVTAVTTV------NKRCLVLANSNVsVEQWRAQFKLW 388
Cdd:cd18007 1 LKPHQVEGVRFLwsnlvgtDVGSDEGGGCILAHTmGLGKTLQVITFLHTYlaaaprRSRPLVLCPAST-LYNWEDEFKKW 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 389 StIQDkqLVRFTREAKDPAPSGADA---------TKPVVCISTYSM-VAYSGRRTLQAEEAMKFIEKQ---EWGLLLLDE 455
Cdd:cd18007 80 L-PPD--LRPLLVLVSLSASKRADArlrkinkwhKEGGVLLIGYELfRNLASNATTDPRLKQEFIAALldpGPDLLVLDE 156
|
170 180 190
....*....|....*....|....*....|.
gi 17556358 456 VHTI--PAKMFRRVLTIVQAHCKLGLTATLV 484
Cdd:cd18007 157 GHRLknEKSQLSKALSKVKTKRRILLTGTPL 187
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
350-482 |
5.42e-03 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 38.81 E-value: 5.42e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 350 GAGKTlvgVTAVTTVN--------KRCLVLANSNVsVEQWraQFKLWSTIQDKQLV--RFTREAKDPAPSGADATKPVVc 419
Cdd:cd18011 27 GLGKT---IEAGLIIKelllrgdaKRVLILCPASL-VEQW--QDELQDKFGLPFLIldRETAAQLRRLIGNPFEEFPIV- 99
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17556358 420 ISTYSMVAYSGRRTLQAEEAmkfiekqEWGLLLLDEVH-------TIPAKMFRRVLTIVQ-AHCKLGLTAT 482
Cdd:cd18011 100 IVSLDLLKRSEERRGLLLSE-------EWDLVVVDEAHklrnsggGKETKRYKLGRLLAKrARHVLLLTAT 163
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
324-422 |
7.89e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 39.86 E-value: 7.89e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556358 324 RPYQEKslrkMFGNSRARSGVIVLPCGAGKTLVG--VTA--VTTVNKRCLVLANSNVSVEQWRAQFKLWSTIQDKQLVRF 399
Cdd:PRK13766 17 RLYQQL----LAATALKKNTLVVLPTGLGKTAIAllVIAerLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVF 92
|
90 100
....*....|....*....|...
gi 17556358 400 TREAKdPAPSGADATKPVVCIST 422
Cdd:PRK13766 93 TGEVS-PEKRAELWEKAKVIVAT 114
|
|
| |
